[English] 日本語
Yorodumi- PDB-3mll: Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mll | ||||||
---|---|---|---|---|---|---|---|
Title | Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide | ||||||
Components | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / ASCORBATE | ||||||
Function / homology | Function and homology information peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / response to pH / mitotic chromosome condensation / L-ascorbic acid binding / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / maternal process involved in female pregnancy / condensed chromosome / response to glucocorticoid / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / chromatin binding / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Chufan, E.E. / Eipper, B.A. / Mains, R.E. / Amzel, L.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Differential reactivity between two copper sites in peptidylglycine alpha-hydroxylating monooxygenase Authors: Chufan, E.E. / Prigge, S.T. / Siebert, X. / Eipper, B.A. / Mains, R.E. / Amzel, L.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mll.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mll.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mll ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mll | HTTPS FTP |
---|
-Related structure data
Related structure data | 3mibC 3micC 3midC 3mieC 3mifC 3migC 3mihC 3mljC 3mlkC 1phmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35008.133 Da / Num. of mol.: 1 / Fragment: UNP residues 43-356, monooxygenase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: SPRAGUE-DAWLEY / Gene: Pam / Plasmid: pCIS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Cho Dg44 / References: UniProt: P14925, peptidylglycine monooxygenase |
---|---|
#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-AZI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization: 0.1-0.5mM CuSO4, 1.25 mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 5mM ascorbic acid and then soaked in 40mM ...Details: Crystallization: 0.1-0.5mM CuSO4, 1.25 mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 5mM ascorbic acid and then soaked in 40mM NaN3 (with 5mM ascorbic acid) for 6 hours at RT., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2007 |
Radiation | Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2. ...Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→52 Å / Num. obs: 6287 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rsym value: 0.088 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 3.25→3.37 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 553 / Rsym value: 0.47 / % possible all: 91.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHM Resolution: 3.25→52 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.848 / SU B: 67.93 / SU ML: 0.53 / Cross valid method: THROUGHOUT / ESU R Free: 0.622 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.994 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.248→3.332 Å / Total num. of bins used: 20
|